Detection and mapping of <scp>QTL</scp> for temperature tolerance and body size in <scp>C</scp>hinook salmon (<i><scp>O</scp>ncorhynchus tshawytscha</i>) using genotyping by sequencing

Everett, Meredith V.; Seeb, James E.

doi:10.1111/eva.12147

Cited by 60 publications

(72 citation statements)

References 71 publications

(147 reference statements)

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“…see comparisons made by Larson et al . to data from Everett & Seeb ). The SbfI recognition sequence is GC‐rich (CCTGCA/GG); this may result in an overrepresentation of SbfI cut sites in gene‐rich regions of the genome.…”

Section: Methodsmentioning

confidence: 97%

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Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

Waples

Seeb

2015

Molecular Ecology Resources

139

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Gene sequence similarity due to shared ancestry after a duplication event, that is paralogy, complicates the assessment of genetic variation, as sequences originating from paralogs can be difficult to distinguish. These confounded sequences are often removed prior to further analyses, leaving the underlying loci uncharacterized. Salmonids have only partially rediploidized subsequent to a whole-genome duplication; residual tetrasomic inheritance has been observed in males. We present a maximum-likelihood-based method to resolve confounded paralogous loci by observing the segregation of alleles in gynogenetic haploid offspring and demonstrate its effectiveness by constructing two linkage maps for chum salmon (Oncorhynchus keta), with and without these newly resolved loci. We find that the resolved paralogous loci are not randomly distributed across the genome. A majority are clustered in expanded subtelomeric regions of 14 linkage groups, suggesting a significant fraction of the chum salmon genome may be missed by the exclusion of paralogous loci. Transposable elements have been proposed as drivers of genome evolution and, in salmonids, may have an important role in the rediploidization process by driving differentiation between homeologous chromosomes. Consistent with that hypothesis, we find a reduced fraction of transposable element annotations among paralogous loci, and these loci predominately occur in the genomic regions that lag in the rediploidization process.

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Section: Methodsmentioning

confidence: 97%

“…We used Stacks parameter values similar to those that have been successfully applied to salmonids and that are generally consistent with published protocols (Everett & Seeb ; Mastretta‐Yanes et al . ).…”

Section: Methodsmentioning

confidence: 99%

Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

Waples

Seeb

2015

Molecular Ecology Resources

139

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“…By scoring the phenotypes of F 1 and F 2 generations and associating this to genetic variation it is possible to identify quantitative trait loci (QTL) responsible for phenotypic traits (Shrimpton and Robertson 1988, Mackay 1995, Erickson et al 2004). However, pedigree crossing is a timely process and many species do not lend themselves to being bred over multiple generations in a laboratory environment (but see Everett and Seeb 2014). Moreover, such studies do not reveal how traits respond to selection in the wild.…”

Section: Towards a Better Understanding Of Plasticity And Adaptationmentioning

confidence: 99%

The importance of phenotypic plasticity and local adaptation in driving intraspecific variability in thermal niches of marine macrophytes

et al. 2017

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Climate change is driving the redistribution of species at a global scale and documenting and predicting species' responses to warming is a principal focus of contemporary ecology. When interpreting and predicting their responses to warming, species are generally treated as single homogenous physiological units. However, local adaptation and phenotypic plasticity can result in intraspecific differences in thermal niche. Therefore, population loss may also not only occur from trailing edges. In species with low dispersal capacity this will have profound impacts for the species as a whole, as local population loss will not be offset by immigration of warm tolerant individuals. Recent evidence from terrestrial forests has shown that incorporation of intraspecific variation in thermal niche is vital to accurately predicting species responses to warming. However, marine macrophytes (i.e. seagrasses and seaweeds) that form some of the world's most productive and diverse ecosystems have not been examined in the same context. We conducted a literature review to determine how common intraspecific variation in thermal physiology is in marine macrophytes. We find that 90% of studies identified (n = 42) found clear differences in thermal niche between geographically separated populations. Therefore, non-trailing edge populations may also be vulnerable to future warming trends and given their limited dispersal capacity, such population loss may not be offset by immigration. We also explore how next generation sequencing (NGS) is allowing unprecedented mechanistic insight into plasticity and adaptation. We conclude that in the 'genomic era' it may be possible to link understanding of plasticity and adaptation at the genetic level through to changes in populations providing novel insights on the redistribution of populations under future climate change.

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“…High-throughput GBS was used to detect and map a few thousand SNPs in haploid Chinook salmon, O. tshawytscha (Everett and Seeb, 2014). This map was used to detect QTL related to temperature tolerance and body size in families of diploid Chinook salmon.…”

Section: Growth Traitsmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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-An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

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Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing

Cited by 60 publications

References 71 publications

Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

The importance of phenotypic plasticity and local adaptation in driving intraspecific variability in thermal niches of marine macrophytes

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

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